Different types of tools are used to perform hundreds of processing operations during semiconductor device fabrication. Most of these operations are performed in vacuum chambers at very low pressure. Substrates, such as semiconductor wafers, are introduced to the process chambers and placed on semiconductor wafer pedestals within the process chambers with wafer handling systems that are mechanically coupled to the process chambers. The wafer handling systems transfer semiconductor wafers from the factory floor to semiconductor wafer pedestals within the process chambers. These systems include loadlocks to bring the semiconductor wafers from atmospheric conditions to very low pressure conditions and back, and robots to transfer the semiconductor wafers to various positions. Accurate orientation of the semiconductor wafers on the semiconductor wafer pedestals is critical to ensure wafers are free of defects. Calibration of the wafer handling systems would also benefit from greater repeatability in the calibration process to ensure consistently accurate calibrations. There is a need for more accurate and repeatable calibration of the wafer handling systems to decrease the number of defects on the semiconductor wafers.